It could be your isolator. The specs say it has a drop out voltage of 12.6V which is under the voltage of a fully charged battery (in theory 12.67V) and certainly less than a recently charged battery (which may be as high as ~13.6V but certainly over 12.7V, and an open circuit battery can take a day to lose that surface charge, or several minutes with lights on.)

So if your batteries are connected and the isolation delay is too long (maybe 4 seconds from what you suggest; usually they are 15-60 seconds), both batteries suffer the cranking dip. (Unlike diode isolators, your MOSFET isolator probably conducts both ways.)

If only some genius could come up with an isolator that is isolated when the car stops charging and doesn't reconnect until after cranking when charging has recommenced. Surely that'd be worth a Nobel Prizeor two?

It could be your isolator. The specs say it has a drop out voltage of 12.6V which is under the voltage of a fully charged battery (in theory 12.67V) and certainly less than a recently charged battery (which may be as high as ~13.6V but certainly over 12.7V, and an open circuit battery can take a day to lose that surface charge, or several minutes with lights on.)

So if your batteries are connected and the isolation delay is too long (maybe 4 seconds from what you suggest; usually they are 15-60 seconds), both batteries suffer the cranking dip. (Unlike diode isolators, your MOSFET isolator probably conducts both ways.)

If only some genius could come up with an isolator that is isolated when the car stops charging and doesn't reconnect until after cranking when charging has recommenced. Surely that'd be worth a Nobel Prizeor two?

I am thinking that you are right. I think that I am seeing two issues. The issue with the power supply and the issue (as you so properly pointed out) with my isolator.

Also you are correct, current does flow both directions although the resistance is much higher flowing from AUX to MAIN.

I am thinking that this isolator has just gotta go and I need something that will accomplish true isolation without being apart of the cranking process.

Do you recommend anything? Also how would you go about finding out if my 2006 Mazda 6 has a charge lamp, that seems like the easiest method

It's a light (not heavy) that comes on with the ignition, should go out after starting, and come on again as soon as the engine stalls.
No to be confused with an oil-pressure lamp that can go out during cranking (as can some rare charge lights) but usually takes a while to relight after stalling (and hence the problem when oil-pressure is used as a SAFETY device for petrol control (pumps, cut-offs etc) and - btw - not that oil pressure should ever cut petrol as a way of preserving the engine!).

Couldn't find one specifically for a mazda 6 but this is what they usually look like:
One of the 4-5 lights that come on when you turn it to ignition but then go out when you start the car.
Once you have found that you will then need to find a wiring diagram for you car to find out how to t into it.

If only some genius could come up with an isolator that is isolated when the car stops charging and doesn't reconnect until after cranking when charging has recommenced. Surely that'd be worth a Nobel Prizeor two?

LOL - yeah, some people still don't get it...
But I suppose you being down-under would be well used to those that think finding the alternator - or a terminal on it - is way too hard - it's much easier buying an 80A Redarc (which I have on good authority will charge a battery more completely and faster than a 120A or 200A relay!!) or some other voltage sensing isolator... hey maybe even the "priority charging" Projecta for a mere $300 or more.
BTW - don't tell people what their dash lights mean - it starves the industry of business.

The simplest way to the charge light is usually at the alternator.
Besides, some vehicles that do not have (dash) charge lights still have the L (or D+) terminal on the alternator.
And further besides, why worry about tapping the dash for something that comes from the alternator, and will probably sit in the engine bay?

It's a light (not heavy) that comes on with the ignition, should go out after starting, and come on again as soon as the engine stalls.
No to be confused with an oil-pressure lamp that can go out during cranking (as can some rare charge lights) but usually takes a while to relight after stalling (and hence the problem when oil-pressure is used as a SAFETY device for petrol control (pumps, cut-offs etc) and - btw - not that oil pressure should ever cut petrol as a way of preserving the engine!).

But I'd suggest you consult your vehicle's owner's manual...

I do have a charge lamp. Could you point me to a schematic so I can consider what is involved.